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PDBsum entry 1jqw

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protein ligands metals links
Signaling protein PDB id
1jqw
Jmol
Contents
Protein chain
150 a.a. *
Ligands
HCS ×3
Metals
_ZN
Waters ×53
* Residue conservation analysis
PDB id:
1jqw
Name: Signaling protein
Title: The 2.3 angstrom resolution structure of bacillus subtilis luxs/homocysteine complex
Structure: Autoinducer-2 production protein luxs. Chain: a. Synonym: s-ribosylhomocysteine lyase, ai-2 synthesis protei engineered: yes. Mutation: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: luxs. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.175     R-free:   0.241
Authors: S.N.Ruzheinikov,S.K.Das,S.E.Sedelnikova,A.Hartley,S.J.Foster M.J.Horsburgh,A.G.Cox,C.W.Mccleod,A.Mekhalfia,G.M.Blackburn D.W.Rice,P.J.Baker
Key ref:
S.N.Ruzheinikov et al. (2001). The 1.2 A structure of a novel quorum-sensing protein, Bacillus subtilis LuxS. J Mol Biol, 313, 111-122. PubMed id: 11601850 DOI: 10.1006/jmbi.2001.5027
Date:
09-Aug-01     Release date:   24-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O34667  (LUXS_BACSU) -  S-ribosylhomocysteine lyase
Seq:
Struc:
157 a.a.
150 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.4.1.21  - S-ribosylhomocysteine lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Autoinducer AI-2 Biosynthesis
      Reaction: S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5- dihydroxypentan-2,3-dione
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine
=
L-homocysteine
Bound ligand (Het Group name = HCS)
corresponds exactly
+ (4S)-4,5- dihydroxypentan-2,3-dione
      Cofactor: Fe(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.5027 J Mol Biol 313:111-122 (2001)
PubMed id: 11601850  
 
 
The 1.2 A structure of a novel quorum-sensing protein, Bacillus subtilis LuxS.
S.N.Ruzheinikov, S.K.Das, S.E.Sedelnikova, A.Hartley, S.J.Foster, M.J.Horsburgh, A.G.Cox, C.W.McCleod, A.Mekhalfia, G.M.Blackburn, D.W.Rice, P.J.Baker.
 
  ABSTRACT  
 
In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. The autoinducer-2 production protein LuxS, is involved in a novel quorum-sensing system and is thought to catalyse the degradation of S-ribosylhomocysteine to homocysteine and the autoinducer molecule 4,5-dihydroxy-2,3-pentadione. The crystal structure of Bacillus subtilis LuxS has been determined at 1.2 A resolution, together with the binary complexes of LuxS with S-ribosylhomocysteine and homocysteine to 2.2 and 2.3 A resolution, respectively. These structures show that LuxS is a homodimer with an apparently novel fold based on an eight-stranded beta-barrel, flanked by six alpha-helices. Each active site contains a zinc ion coordinated by the conserved residues His54, His58 and Cys126, and includes residues from both subunits. S-ribosylhomocysteine binds in a deep pocket with the ribose moiety adjacent to the enzyme-bound zinc ion. Access to the active site appears to be restricted and possibly requires conformational changes in the protein involving the movement of residues 125-129 and those at the N terminus. The structure contains an oxidised cysteine residue in the active site whose role in the biological process of LuxS has not been determined. The autoinducer-2 signalling pathway has been linked to aspects of bacterial virulence and pathogenicity. The structural data on LuxS will provide opportunities for targeting this enzyme for the rational design of new antibiotics.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Luxs catalysed degradation of S-ribosylhomocysteine to homocysteine and the autoinducer molecule 4,5-dihydroxy-2,3-pentadione.
Figure 3.
Figure 3. (a) A stereo representation of the structure of the LuxS dimer. The Zn2+ is shown in the two active sites as a magenta sphere. The position of ribosylhomocysteine is indicated (RHC) as is the homocysteine bound to Cys41 (HC). (b) A stereo diagram of the van der Waals surface of the LuxS dimer (calculated by rolling ball with a radius of 1.4 Å). One monomer is coloured according to the electrostatic potential, and the other grey. The Zn2+ is shown in the two active sites of the dimer as a green sphere. The Figure was made with WebLabViewerPro4.0.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 313, 111-122) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264316 P.Plummer, J.Zhu, M.Akiba, D.Pei, and Q.Zhang (2011).
Identification of a key amino acid of LuxS involved in AI-2 production in Campylobacter jejuni.
  PLoS One, 6, e15876.  
20704697 M.Bhattacharyya, and S.Vishveshwara (2010).
Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis.
  BMC Struct Biol, 10, 27.  
19754952 G.Kint, K.A.Sonck, G.Schoofs, D.De Coster, J.Vanderleyden, and S.C.De Keersmaecker (2009).
2D proteome analysis initiates new Insights on the Salmonella Typhimurium LuxS protein.
  BMC Microbiol, 9, 198.  
19243584 M.Bhattacharyya, and S.Vishveshwara (2009).
Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks.
  BMC Struct Biol, 9, 8.  
19411415 M.Zhang, X.D.Jiao, Y.H.Hu, and L.Sun (2009).
Attenuation of Edwardsiella tarda virulence by small peptides that interfere with LuxS/autoinducer type 2 quorum sensing.
  Appl Environ Microbiol, 75, 3882-3890.  
18956421 N.Ni, M.Li, J.Wang, and B.Wang (2009).
Inhibitors and antagonists of bacterial quorum sensing.
  Med Res Rev, 29, 65.  
19594442 S.Raina, D.D.Vizio, M.Odell, M.Clements, S.Vanhulle, and T.Keshavarz (2009).
Microbial quorum sensing: a tool or a target for antimicrobial therapy?
  Biotechnol Appl Biochem, 54, 65-84.  
19775890 T.Zang, B.W.Lee, L.M.Cannon, K.A.Ritter, S.Dai, D.Ren, T.K.Wood, and Z.S.Zhou (2009).
A naturally occurring brominated furanone covalently modifies and inactivates LuxS.
  Bioorg Med Chem Lett, 19, 6200-6204.  
17056751 M.F.Hullo, S.Auger, O.Soutourina, O.Barzu, M.Yvon, A.Danchin, and I.Martin-Verstraete (2007).
Conversion of methionine to cysteine in Bacillus subtilis and its regulation.
  J Bacteriol, 189, 187-197.  
  17869606 Y.Turovskiy, D.Kashtanov, B.Paskhover, and M.L.Chikindas (2007).
Quorum sensing: fact, fiction, and everything in between.
  Adv Appl Microbiol, 62, 191-234.  
16740951 E.Lombardía, A.J.Rovetto, A.L.Arabolaza, and R.R.Grau (2006).
A LuxS-dependent cell-to-cell language regulates social behavior and development in Bacillus subtilis.
  J Bacteriol, 188, 4442-4452.  
16897563 F.C.Petersen, N.A.Ahmed, A.Naemi, and A.A.Scheie (2006).
LuxS-mediated signalling in Streptococcus anginosus and its role in biofilm formation.
  Antonie Van Leeuwenhoek, 90, 109-121.  
17158701 J.E.González, and N.D.Keshavan (2006).
Messing with bacterial quorum sensing.
  Microbiol Mol Biol Rev, 70, 859-875.  
16597969 S.Challan Belval, L.Gal, S.Margiewes, D.Garmyn, P.Piveteau, and J.Guzzo (2006).
Assessment of the roles of LuxS, S-ribosyl homocysteine, and autoinducer 2 in cell attachment during biofilm formation by Listeria monocytogenes EGD-e.
  Appl Environ Microbiol, 72, 2644-2650.  
15864263 A.Vendeville, K.Winzer, K.Heurlier, C.M.Tang, and K.R.Hardie (2005).
Making 'sense' of metabolism: autoinducer-2, LuxS and pathogenic bacteria.
  Nat Rev Microbiol, 3, 383-396.  
15255890 K.M.Pappas, C.L.Weingart, and S.C.Winans (2004).
Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling.
  Mol Microbiol, 53, 755-769.  
15175279 S.C.Winans (2004).
Reciprocal regulation of bioluminescence and type III protein secretion in Vibrio harveyi and Vibrio parahaemolyticus in response to diffusible chemical signals.
  J Bacteriol, 186, 3674-3676.  
12654815 J.Merritt, F.Qi, S.D.Goodman, M.H.Anderson, and W.Shi (2003).
Mutation of luxS affects biofilm formation in Streptococcus mutans.
  Infect Immun, 71, 1972-1979.  
12117917 B.Stevenson, and K.Babb (2002).
LuxS-mediated quorum sensing in Borrelia burgdorferi, the lyme disease spirochete.
  Infect Immun, 70, 4099-4105.  
  12537600 M.P.DeLisa, and W.E.Bentley (2002).
Bacterial autoinduction: looking outside the cell for new metabolic engineering targets.
  Microb Cell Fact, 1, 5.  
12399491 M.Roessler, and V.Müller (2002).
Chloride, a new environmental signal molecule involved in gene regulation in a moderately halophilic bacterium, Halobacillus halophilus.
  J Bacteriol, 184, 6207-6215.  
12223068 P.Williams (2002).
Quorum sensing: an emerging target for antibacterial chemotherapy?
  Expert Opin Ther Targets, 6, 257-274.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.